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root/OpenMD/branches/development/src/selection/SelectionEvaluator.cpp

Comparing:
trunk/src/selection/SelectionEvaluator.cpp (file contents), Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs.
branches/development/src/selection/SelectionEvaluator.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	+	#include <stack>
44		#include "selection/SelectionEvaluator.hpp"
45	<	namespace oopse {
45	>	#include "primitives/Atom.hpp"
46	>	#include "primitives/DirectionalAtom.hpp"
47	>	#include "primitives/RigidBody.hpp"
48	>	#include "primitives/Molecule.hpp"
49	>	#include "io/ifstrstream.hpp"
50	>
51	>	namespace OpenMD {
52	>
53	>
54	>	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
55	>	: info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
56	>	indexFinder(info),
57	>	isLoaded_(false){
58	>	nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
59	>	}
60	>
61	>	bool SelectionEvaluator::loadScript(const std::string& filename,
62	>	const std::string& script) {
63	>	clearDefinitionsAndLoadPredefined();
64	>	this->filename = filename;
65	>	this->script = script;
66	>	if (! compiler.compile(filename, script)) {
67	>	error = true;
68	>	errorMessage = compiler.getErrorMessage();
69	>
70	>	sprintf( painCave.errMsg,
71	>	"SelectionCompiler Error: %s\n", errorMessage.c_str());
72	>	painCave.severity = OPENMD_ERROR;
73	>	painCave.isFatal = 1;
74	>	simError();
75	>	return false;
76	>	}
77	>
78	>	pc = 0;
79	>	aatoken = compiler.getAatokenCompiled();
80	>	linenumbers = compiler.getLineNumbers();
81	>	lineIndices = compiler.getLineIndices();
82	>
83	>	std::vector<std::vector<Token> >::const_iterator i;
84	>
85	>	isDynamic_ = false;
86	>	for (i = aatoken.begin(); i != aatoken.end(); ++i) {
87	>	if (containDynamicToken(*i)) {
88	>	isDynamic_ = true;
89	>	break;
90	>	}
91	>	}
92	>
93	>	isLoaded_ = true;
94	>	return true;
95	>	}
96	>
97	>	void SelectionEvaluator::clearState() {
98	>	error = false;
99	>	errorMessage = "";
100	>	}
101	>
102	>	bool SelectionEvaluator::loadScriptString(const std::string& script) {
103	>	clearState();
104	>	return loadScript("", script);
105	>	}
106	>
107	>	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
108	>	clearState();
109	>	return loadScriptFileInternal(filename);
110	>	}
111	>
112	>	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
113	>	ifstrstream ifs(filename.c_str());
114	>	if (!ifs.is_open()) {
115	>	return false;
116	>	}
117	>
118	>	const int bufferSize = 65535;
119	>	char buffer[bufferSize];
120	>	std::string script;
121	>	while(ifs.getline(buffer, bufferSize)) {
122	>	script += buffer;
123	>	}
124	>	return loadScript(filename, script);
125	>	}
126	>
127	>	void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){
128	>
129	>	while ( pc < aatoken.size()) {
130	>	statement = aatoken[pc++];
131	>	statementLength = statement.size();
132	>	Token token = statement[0];
133	>	switch (token.tok) {
134	>	case Token::define:
135	>	define();
136	>	break;
137	>	case Token::select:
138	>	select(bs);
139	>	break;
140	>	default:
141	>	unrecognizedCommand(token);
142	>	return;
143	>	}
144	>	}
145	>
146	>	}
147	>
148	>	OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
149	>	int pcStart) {
150	>	OpenMDBitSet bs;
151	>	std::stack<OpenMDBitSet> stack;
152	>
153	>	for (int pc = pcStart; pc < code.size(); ++pc) {
154	>	Token instruction = code[pc];
155	>
156	>	switch (instruction.tok) {
157	>	case Token::expressionBegin:
158	>	break;
159	>	case Token::expressionEnd:
160	>	break;
161	>	case Token::all:
162	>	bs = OpenMDBitSet(nStuntDouble);
163	>	bs.setAll();
164	>	stack.push(bs);
165	>	break;
166	>	case Token::none:
167	>	bs = OpenMDBitSet(nStuntDouble);
168	>	stack.push(bs);
169	>	break;
170	>	case Token::opOr:
171	>	bs = stack.top();
172	>	stack.pop();
173	>	stack.top() |= bs;
174	>	break;
175	>	case Token::opAnd:
176	>	bs = stack.top();
177	>	stack.pop();
178	>	stack.top() &= bs;
179	>	break;
180	>	case Token::opNot:
181	>	stack.top().flip();
182	>	break;
183	>	case Token::within:
184	>	withinInstruction(instruction, stack.top());
185	>	break;
186	>	case Token::hull:
187	>	stack.push(hull());
188	>	break;
189	>	//case Token::selected:
190	>	//  stack.push(getSelectionSet());
191	>	//  break;
192	>	case Token::name:
193	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
194	>	break;
195	>	case Token::index:
196	>	stack.push(indexInstruction(instruction.value));
197	>	break;
198	>	case Token::identifier:
199	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
200	>	break;
201	>	case Token::opLT:
202	>	case Token::opLE:
203	>	case Token::opGE:
204	>	case Token::opGT:
205	>	case Token::opEQ:
206	>	case Token::opNE:
207	>	stack.push(comparatorInstruction(instruction));
208	>	break;
209	>	default:
210	>	unrecognizedExpression();
211	>	}
212	>	}
213	>	if (stack.size() != 1)
214	>	evalError("atom expression compiler error - stack over/underflow");
215	>
216	>	return stack.top();
217	>	}
218	>
219	>
220	>
221	>	OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
222	>	int comparator = instruction.tok;
223	>	int property = instruction.intValue;
224	>	float comparisonValue = boost::any_cast<float>(instruction.value);
225	>	float propertyValue;
226	>	OpenMDBitSet bs(nStuntDouble);
227	>	bs.clearAll();
228	>
229	>	SimInfo::MoleculeIterator mi;
230	>	Molecule* mol;
231	>	Molecule::AtomIterator ai;
232	>	Atom* atom;
233	>	Molecule::RigidBodyIterator rbIter;
234	>	RigidBody* rb;
235	>
236	>	for (mol = info->beginMolecule(mi); mol != NULL;
237	>	mol = info->nextMolecule(mi)) {
238	>
239	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
240	>	compareProperty(atom, bs, property, comparator, comparisonValue);
241	>	}
242	>
243	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
244	>	rb = mol->nextRigidBody(rbIter)) {
245	>	compareProperty(rb, bs, property, comparator, comparisonValue);
246	>	}
247	>	}
248	>
249	>	return bs;
250	>	}
251	>
252	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
253	>	int property, int comparator,
254	>	float comparisonValue) {
255	>	RealType propertyValue = 0.0;
256	>	switch (property) {
257	>	case Token::mass:
258	>	propertyValue = sd->getMass();
259	>	break;
260	>	case Token::charge:
261	>	if (sd->isAtom()){
262	>	Atom* atom = static_cast<Atom*>(sd);
263	>	propertyValue = getCharge(atom);
264	>	} else if (sd->isRigidBody()) {
265	>	RigidBody* rb = static_cast<RigidBody*>(sd);
266	>	RigidBody::AtomIterator ai;
267	>	Atom* atom;
268	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
269	>	propertyValue+=  getCharge(atom);
270	>	}
271	>	}
272	>	break;
273	>	case Token::x:
274	>	propertyValue = sd->getPos().x();
275	>	break;
276	>	case Token::y:
277	>	propertyValue = sd->getPos().y();
278	>	break;
279	>	case Token::z:
280	>	propertyValue = sd->getPos().z();
281	>	break;
282	>	case Token::r:
283	>	propertyValue = sd->getPos().length();
284	>	break;
285	>	default:
286	>	unrecognizedAtomProperty(property);
287	>	}
288	>
289	>	bool match = false;
290	>	switch (comparator) {
291	>	case Token::opLT:
292	>	match = propertyValue < comparisonValue;
293	>	break;
294	>	case Token::opLE:
295	>	match = propertyValue <= comparisonValue;
296	>	break;
297	>	case Token::opGE:
298	>	match = propertyValue >= comparisonValue;
299	>	break;
300	>	case Token::opGT:
301	>	match = propertyValue > comparisonValue;
302	>	break;
303	>	case Token::opEQ:
304	>	match = propertyValue == comparisonValue;
305	>	break;
306	>	case Token::opNE:
307	>	match = propertyValue != comparisonValue;
308	>	break;
309	>	}
310	>	if (match)
311	>	bs.setBitOn(sd->getGlobalIndex());
312	>
313	>	}
314
315	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
316	+	OpenMDBitSet& bs){
317	+
318	+	boost::any withinSpec = instruction.value;
319	+	float distance;
320	+	if (withinSpec.type() == typeid(float)){
321	+	distance = boost::any_cast<float>(withinSpec);
322	+	} else if (withinSpec.type() == typeid(int)) {
323	+	distance = boost::any_cast<int>(withinSpec);
324	+	} else {
325	+	evalError("casting error in withinInstruction");
326	+	bs.clearAll();
327	+	}
328	+
329	+	bs = distanceFinder.find(bs, distance);
330	+	}
331	+
332	+	void SelectionEvaluator::define() {
333	+	assert(statement.size() >= 3);
334	+
335	+	std::string variable = boost::any_cast<std::string>(statement[1].value);
336	+
337	+	variables.insert(VariablesType::value_type(variable,
338	+	expression(statement, 2)));
339	+	}
340	+
341
342	+	/** @todo */
343	+	void SelectionEvaluator::predefine(const std::string& script) {
344	+
345	+	if (compiler.compile("#predefine", script)) {
346	+	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
347	+	if (aatoken.size() != 1) {
348	+	evalError("predefinition does not have exactly 1 command:"
349	+	+ script);
350	+	return;
351	+	}
352	+	std::vector<Token> statement = aatoken[0];
353	+	if (statement.size() > 2) {
354	+	int tok = statement[1].tok;
355	+	if (tok == Token::identifier ||
356	+	(tok & Token::predefinedset) == Token::predefinedset) {
357	+	std::string variable = boost::any_cast<std::string>(statement[1].value);
358	+	variables.insert(VariablesType::value_type(variable, statement));
359	+
360	+	} else {
361	+	evalError("invalid variable name:" + script);
362	+	}
363	+	}else {
364	+	evalError("bad predefinition length:" + script);
365	+	}
366	+
367	+	} else {
368	+	evalError("predefined set compile error:" + script +
369	+	"\ncompile error:" + compiler.getErrorMessage());
370	+	}
371	+	}
372	+
373	+	void SelectionEvaluator::select(OpenMDBitSet& bs){
374	+	bs = expression(statement, 1);
375	+	}
376	+
377	+	OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
378	+
379	+	OpenMDBitSet bs(nStuntDouble);
380	+	std::map<std::string, boost::any>::iterator i = variables.find(variable);
381	+
382	+	if (i != variables.end()) {
383	+	if (i->second.type() == typeid(OpenMDBitSet)) {
384	+	return boost::any_cast<OpenMDBitSet>(i->second);
385	+	} else if (i->second.type() ==  typeid(std::vector<Token>)){
386	+	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
387	+	i->second =  bs; /**@todo fixme */
388	+	return bs;
389	+	}
390	+	} else {
391	+	unrecognizedIdentifier(variable);
392	+	}
393	+
394	+	return bs;
395	+	}
396	+
397	+	OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){
398	+	return nameFinder.match(name);
399	+	}
400	+
401	+	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
402	+	std::vector<Token>::const_iterator i;
403	+	for (i = tokens.begin(); i != tokens.end(); ++i) {
404	+	if (i->tok & Token::dynamic) {
405	+	return true;
406	+	}
407	+	}
408	+
409	+	return false;
410	+	}
411	+
412	+	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
413	+	variables.clear();
414	+	//load predefine
415	+	//predefine();
416	+	}
417	+
418	+	OpenMDBitSet SelectionEvaluator::evaluate() {
419	+	OpenMDBitSet bs(nStuntDouble);
420	+	if (isLoaded_) {
421	+	pc = 0;
422	+	instructionDispatchLoop(bs);
423	+	}
424	+
425	+	return bs;
426	+	}
427	+
428	+	OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
429	+	OpenMDBitSet bs(nStuntDouble);
430	+
431	+	if (value.type() == typeid(int)) {
432	+	int index = boost::any_cast<int>(value);
433	+	if (index < 0 || index >= bs.size()) {
434	+	invalidIndex(index);
435	+	} else {
436	+	bs = indexFinder.find(index);
437	+	}
438	+	} else if (value.type() == typeid(std::pair<int, int>)) {
439	+	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
440	+	assert(indexRange.first <= indexRange.second);
441	+	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
442	+	invalidIndexRange(indexRange);
443	+	}else {
444	+	bs = indexFinder.find(indexRange.first, indexRange.second);
445	+	}
446	+	}
447	+
448	+	return bs;
449	+	}
450	+
451	+
452	+	OpenMDBitSet SelectionEvaluator::hull() {
453	+	OpenMDBitSet bs(nStuntDouble);
454	+
455	+	bs = hullFinder.findHull();
456	+
457	+	return bs;
458	+	}
459	+
460	+
461	+
462	+	RealType SelectionEvaluator::getCharge(Atom* atom) {
463	+	RealType charge =0.0;
464	+	AtomType* atomType = atom->getAtomType();
465	+	if (atomType->isCharge()) {
466	+	GenericData* data = atomType->getPropertyByName("Charge");
467	+	if (data != NULL) {
468	+	DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
469	+
470	+	if (doubleData != NULL) {
471	+	charge = doubleData->getData();
472	+
473	+	} else {
474	+	sprintf( painCave.errMsg,
475	+	"Can not cast GenericData to DoubleGenericData\n");
476	+	painCave.severity = OPENMD_ERROR;
477	+	painCave.isFatal = 1;
478	+	simError();
479	+	}
480	+	}
481	+	}
482	+
483	+	return charge;
484	+	}
485	+
486		}

Comparing:
trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords), Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs.
branches/development/src/selection/SelectionEvaluator.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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